The cover issued on Saturday featured a black and white photograph of Macron standing against a red background, with an image of Yellow Vest protesters surging towards the Arc de Triomphe.
The magazine’s readers were quick to draw comparisons between the photo and an illustration of Adolf Hitler by artist Lincoln Agnew.
The choice to depict the magazine's M logo in a black, Gothic font, similar to the Nazi swastika, also drew the ire of critics.
On social networks, users expressed their sense of bewilderment at the cover's intentions, including the President of the National Assembly Richard Ferrand.
Hâte de comprendre ce qui fonde les références graphiques et iconographiques du @lemonde_M S’il ne peut s’agir de hasard, de quoi s’agit-il alors ? À la recherche du sens perdu... pic.twitter.com/MHMmia0G2cRichard Ferrand (@RichardFerrand) 29 décembre 2018
“Looking forward to understanding what underlies the graphic and iconographic references of @lemonde_M. If it cannot be a matter of chance, what is it then? In search of the lost meaning…” he wrote in French.
The magazine insisted that it had no intention to compare Macron to the Nazi leader.
“We apologize to those who have been shocked by the graphic design which obviously does not correspond to the reproaches forwarded to us,” Luc Bronner, Chief Editor of M magazine, explained in an editorial note.
Bronner added that the cover had been inspired by works of Russian constructivists, who also "used black and red", he said, recalling that the artist, Lincoln Agnew, had previously designed several magazine covers in a similar style.
But not everyone saw the Hitler likeness. Some Twitter users suggested Le Monde was actually comparing Macron to the Communism ideologist Karl Marx.
The controversy comes amid Yellow Vest protests that have been going on since mid-November, although they now appear to be losing steam.
Macron is due to address the French nation on Monday 31 December to respond to the crisis and try and turn the page on a tumultuous year.